BMC Genomics最新文献

Background: GATA transcription factors are ubiquitous in plants, where they regulate target gene expression to modulate plant growth, development, and responses to environmental stresses. The GATA gene family has been identified in numerous plant species, with characterization reported in cucumber and melon among Cucurbitaceae crops. However, the GATA gene family remains unstudied in most other Cucurbitaceae species. Here, we systematically identified GATA genes in 10 Cucurbitaceae species (watermelon, cucumber, melon, pumpkin, wax gourd, sponge gourd, bottle gourd, bitter gourd, chayote, snake gourd) using the latest high-quality genomic datasets.

Results: A total of 281 GATA genes were identified across these 10 species, and phylogenetic analysis clustered them into four subgroups (Groups A, B, C, D). For watermelon GATA (ClGATA) genes, cis-acting element analysis revealed abundant stress-responsive elements in their promoter regions. Predictions of ClGATA protein secondary and tertiary structures showed random coils as the dominant secondary structural component, with subgroup-specific tertiary characteristics supporting functional synergy within each subgroup. Intraspecific synteny analysis identified 7 segmentally duplicated ClGATA gene pairs, with no tandem duplications detected, indicating segmental duplication drove the expansion of the ClGATA family. Transcriptome reanalysis under 17 types of abiotic and biotic stresses showed ClGATA7 exhibited significant differential expression under 5 abiotic and 3 biotic stress types, and ClGATA11 showed significant differential expression under 3 abiotic and 5 biotic stress types. Quantitative real-time PCR (qRT-PCR) validation of 6 key ClGATA genes further confirmed the role of ClGATA7 in mediating abiotic stress responses, with consistent down-regulation under low temperature in both leaf and root tissues. Protein-protein interaction prediction identified potential interactions among 21 of the 24 ClGATA proteins, including a direct interaction between ClGATA7 and ClGATA17.

Conclusions: These findings advance our understanding of GATA gene family evolution and function in Cucurbitaceae. Given the broad stress responsiveness of ClGATA7 and ClGATA11, they are highlighted as priority candidate genes for functional studies and genetic improvement of stress tolerance in watermelon.

Background: Sheep have diversified into distinct breeds worldwide through both natural adaptation and human-driven selection, with hybridization serving as an effective strategy for rapid trait improvement. The Tianhua mutton sheep (TMS) is a novel breed derived from crossing South African Mutton Merino (SAMM) with Gansu alpine fine-wool sheep (GAFS). After nearly two decades of selective breeding, TMS has developed great meat quality traits and impressive cold tolerance at high altitudes. To study the genetic mechanism and provide new insights into phenotypic variation, we analyzed the genetic diversity, population structure, and selective signatures of TMS based on whole-genome sequencing of 55 TMS, 11 SAMM, and 197 public sheep genomes worldwide.

Results: Population genetic analysis revealed that TMS forms a distinct branch, with a pedigree composition showing an approximate 5:3 ratio of SAMM to GAFS lineages, consistent with the breeding design. Genetic diversity assessment showed that TMS exhibits higher genetic diversity and a lower inbreeding coefficient than commercial sheep from Africa, the Americas, and Europe, suggesting that TMS has considerable breeding potential to be tapped. Genome-wide scanning using the F_ST and XP-EHH methods was also performed to detect the signatures of selection in TMS, with significance thresholds set at Z(F_ST) >2.57 and XP-EHH >2.31. Functional annotation analysis revealed that the selected genes were related to meat quality traits, high-altitude adaptation, and disease resistance. Specifically, genes such as PLA2G10, SAMD12, CKMT2, ACOT12, and TNS3 are implicated in the processes related to fat metabolism. ZNF280D, RANBP3L, CSRP1, TNNI1, and AGBL4 are related to muscle growth and development. ABCB1 regulates energy metabolism via ATP transport to enhances low-oxygen adaptation, while NOTCH3, FBXO32, and LAMA1 regulate cardiopulmonary function and reduce pulmonary hypertension. Additionally, ATM, GALNTL6, and B4GALT5 may improve disease resistance and enhance environmental adaptability.

Conclusion: The results provide valuable insights for investigating the genetic mechanisms underlying TMS fine traits, enhancing TMS breeding, and developing mutton sheep suited to high-altitude and cold environments. Furthermore, it also indicates that hybrid breeding represents an effective strategy to provide a source of phenotypic variation for local adaptation and rapid acquisition of agronomically important traits.

The European black pine (Pinus nigra J. F. Arnold) is a conifer of high economic and ecological importance and is considered a potential alternative to several forest tree species in Central Europe to support adaptation to global climate warming. However, the fungus Diplodia sapinea (Fr.) Fuckel is causing severe damage and world-wide economic loss to this and other Pinus host species. The lack of genomic resources and the scarce knowledge of the tree´s molecular defense mechanisms limit any breeding perspectives. Here, we report the results of a controlled infection experiment in which the transcriptomic and metabolomic profiles of mock and infected P. nigra saplings from two provenances were compared over a period of 21 days. This combined approach suggests that P. nigra response to D. sapinea infection is activated between 8 and 21 days post-inoculation when key plant defense signaling hormones such as jasmonic acid, abscisic acid and salicylic acid increased. This concurred with high differential gene expression, including the activation of major plant defense-related pathways, leading to the induction of several phytoalexins and defense-related proteins. Furthermore, some of these responses were provenance-specific. Finally, this study identified key genes and metabolic pathways involved in the defense response of P. nigra to D. sapinea, providing a solid basis for further exploration of genetic variation among natural populations (provenances) of different subspecies with varying constitutive and induced defense responses. This deeper understanding will aid in elucidating resistance mechanisms and guiding the selection of plant reproductive material for future forest plantations.

Background: During a latent tuberculosis infection, there exists a dynamic equilibrium between the host and the 'dormant' bacterium wherein they mutually influence each other. An understanding of the host genetic response to 'dormant' tubercle bacilli during infection is necessary for developing targeted strategies against them.

Results: A previously established infection model based on Vitamin C-induced Mtb dormancy was utilized in the present study to identify host responses to 'dormant' Mycobacterium tuberculosis (Mtb) infection by analyzing host transcriptomic data generated from Mtb-infected THP-1 cells. Principal Component Analysis and hierarchical cluster analysis of expression profiles in three cell infection models, namely, 'Active Mtb' (no treatment), 'Vitamin C Mtb' (Vitamin C treatment), and 'Vit C-induced Dormant Mtb' (Vitamin C and isoniazid treatment) infection models at 2-, 24- and 96-hours (h) post-Mtb-infection revealed a discrete clustering of host responses. Co-treatment of infected cells with Vitamin C and isoniazid enabled the capture of host transcriptome response to exclusively 'dormant' (isoniazid-tolerant) bacteria. Pleiotropic modulations in host pathways were observed at 96 h that were either unique to the 'Vit C-induced Dormant Mtb' model or common to the 'Vit C-induced Dormant Mtb' and 'Active Mtb' models of infection. Unique pathways identified in the 'Vit C-induced Dormant Mtb' model included (i) induction of antigen processing and presentation for promotion of host defense machinery, and (ii) decreased expression of genes in 'Fanconi anemia' and 'Homologous Recombination' pathways, indicating an impairment of DNA damage responses. Pathways that were commonly involved in 'Vit C-induced Dormant Mtb' and 'Active Mtb' models included (i) suppression of p53 signaling pathway resulting in a downregulation of pro-apoptotic factors and inhibition of cell apoptosis, (ii) upregulation of p57 leading to cell cycle arrest at the G0/G1 phase and subsequent suppression of DNA replication, and (iii) induction of IDO/TDO-mediated tryptophan catabolism.

Conclusions: Host transcriptome analysis of Mtb-infected cells has revealed that key pathways involved in immune surveillance, DNA repair, and apoptosis are altered, leading to an environment that favors infection. Despite these perturbations, the induction of antigen processing and presentation pathways in the 'Vit C-induced Dormant Mtb' model suggests an attempt by the host to counteract infection. These findings provide valuable insights into how the host cellular environment undergoes extensive modifications during Mtb infection and thereby creates conditions that support bacterial persistence.